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Research Services - Bioinformatics Analysis Core
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Overview | Services | About | FAQ | Policies | Scheduling | Contact
| Bioinformatics Analysis Core | | | | | The Bioinformatics Analysis Core (BAC) offers informed and objective bioinformatics analysis of high-dimensional data from studies that use microarrays, SNP arrays, mass-spectrometry based Proteomics and other high-dimensional data sources including mined biomedical (clinical and demographic) variables. We have expertise in disease prediction modeling, including survivorship models, and offer aid with experimental design through multivariate balancing for patient accrual and case/control selection. We conduct power analyses when realistically possible. We interface and collaborate with GPCL-BAC-affiliated faculty in the departments of Computer Science, Human Genetics, Biomedical Informatics, Biostatistics, Computational Biology and the Center for Computational Biology & Bioinformatics for data analysis, grant writing, manuscript preparation and research presentation production. Other services include development of de novo algorithms to solve challenging biological and biomedical informatics problems.
The BAC is sponsored, in part, by the University of Pittsburgh Clinical and Translational Science Institute. | | | | Services | | | | | Study Design
We work closely with the data acquisition facilities and the investigators to review the robustness of each study design. We employ rigorous methods to help investigators maximize their statistical power via case/control selection and treatment/control selection. In addition, we provide Decision Modeling to help investigators maximize their success in integrative translational studies.
Microarray Data Analysis
We provide data analysis support for basic, translational and clinical research. The analyses are available for studies focused on Alternative Splicing, Association Studies, Biomarker Discovery, Chromosomal Copy Number/LOH, Gene Expression, Gene Regulation and Linkage Studies.
Proteomic Data Analysis
We provide data analysis support for basic, translational, and clinical studies focused on mass-spectrometry based proteomic profiling, biomarker discovery, protein and peptide identification and post-translational modification analysis. We have highly developed expertise in multiplexed and integrative biomarker studies.
Clinical and Demographic Data Mining
We routinely support projects that integrate heterogeneous data types into prediction models, including studies that integrate genetic, genomic, or proteomic data with clinical data.
Prediction Modeling
We provide prediction model optimization using any type of categorical or continuous data. Our analyses include, but are not limited to, biomarker-based detection, diagnosis and survivorship prediction modeling.
Decision Modeling
We provide insight on Integrative Translational Research Study Design by Naive Decision Modeling using our Clinical Decision Modeling System (CDMS).
Algorithm/Software Development
We employ programmer/analysts to construct source code for solving computationally intensive analysis problems. This Scientific Director will consult with you to help you determine whether your analysis problem requires additional development effort.
Research Services
In addition to executing analyses, our staff is trained to participate in the interpretation of results, contribution to of methods, results and conclusions sections of research manuscripts and grant proposals in a timely manner.
| | | | About the Facility | | | | | The GPCL Bioinformatics Analysis Core is located on the 3rd floor of 3343 Forbes Ave (Room 307) while serving the entire University of Pittsburgh campus. The purposes of the core is to provide data analysis, research services (grant section writing and manuscript methods and results section preparation), to participate in research program development as a fully mature Bioinformatics Core, to provide algorithm development and optimization, and to create software that implements best-of-breed algorithms for each of the data sources produced by data production facilities across the University of Pittsburgh campus. | | | | Bioinformatics Analysis Core FAQ | | | | | Q: How do I get started using the Core?
A: Register with myGPCL and send us a Project Initiation Form.
Q: Are these services free to University Investigators?
A: The BAC is a fee-for-service cost recovery center.
Q: What if the analysis results show nothing?
A: We remain impartial to the outcome of our analyses. In certain circumstances we can illustrate definitively what the expected outcome of an analysis would be if there were, in fact, negative results.
Q: How are results reported?
A: Investigators receive a preliminary PPT summary of the results. After a face-to-face consultation to review the results, we may then proceed with further follow-up analyses. After a definitive conclusion is reached, we either provide a written report, or we participate in paper co-authorship and/or grant writing.
Q: What is the expected turn-around time?
A: That depends on the scope and scale of the project. The Core Scientific director provides an estimate during the initial consultation. | | | | Policies | | | | | Confidentiality
GPCL staff will maintain strict confidentiality of research projects for the investigators using the facility. The Bioinformatics Analysis Core will only analyze de-identified data to insure that confidentiality is maintained in line with IRB regulations and requirements and HIPAA guidelines.
Publication Participation
Bioinformatics analysis is at the core of interpretation of data from complex studies. Our philosophy is that we must be prepared to stand behind the results we generate. Thus, it is in the interest of investigators to include BAC staff involved in their projects on manuscripts as co-authors. We will be responsive in a timely manner to request for edits, updated information, and any other reasonable request. We will not participate in the publication of purposively misleading data analysis results. We request that a copy of published scientific papers and reprints be forwarded to the Core Director for all publications that derive from the effort of our staff.
Support Letter
The Scientific Director will gladly provide investigators with a letter of support stating our willingness to assist you with your research. Please contact the Core Administrator for more information.
Billing
Billing is done on a monthly basis. For internal users, billing will be done automatically by interdepartmental charges (IDC). Users outside the university will receive an invoice by mail.
Approval
IRB approval must be obtained prior to undertaking the analysis of data for any research project involving human subjects. You are responsible to assure that your IRB approval is current and covers the samples and analyses that you are performing or asking us to perform.
| | | | Scheduling | | | | | After registering (link) as a PI on the GPCL website, you can schedule an initial consultation by contacting the BAC scientific director James Lyons-Weiler by phone at 412-383-2087 or 412-728-8743 or by email. The Bioinformatics Director will meet with you to discuss the scope of the project, including an assessment of your study design, provide an initial cost estimate, and discuss the analysis schedule. Follow-up meetings will occur as needed during the scheduled period until project completion. | | | | Contact Us | | | | | You may contact us at our main office or contact the Bioinformatics Analysis Core directly.
James Lyons-Weiler
Scientific Director
Bioinformatics Analysis Core
(412) 393-2087 (office)
(412) 728-8743 (cell)
Fax: 412-648-1891
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